SAXSdb — 7xe3

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific histone demethylase 1B

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 30–822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 8A2 3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal × 1 FLC CITRATE ANION × 1 PG4 TETRAETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；330mM Ammonium citrate, 26% PEG 3350	Resolution 2.82 Å R-free 0.222
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 30–822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 8A2 3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；330mM Ammonium citrate, 26% PEG 3350	Resolution 2.82 Å R-free 0.222

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 7XE3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FWE Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A Deposited 2012-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；289 K；21% PEG3350, 200mM diammonium citrate, pH 7, EVAPORATION, temperature 289K	Resolution 2.13 Å R-free 0.246
4FWE Native structure of LSD2 /AOF1/KDM1b in spacegroup of C2221 at 2.13A Deposited 2012-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 6 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 FLC CITRATE ANION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；289 K；21% PEG3350, 200mM diammonium citrate, pH 7, EVAPORATION, temperature 289K	Resolution 2.13 Å R-free 0.246
4FWF Complex structure of LSD2/AOF1/KDM1b with H3K4 mimic Deposited 2012-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；21% PEG3350, 200mM diammonium citrate, pH 7, VAPOR DIFFUSION, temperature 298K	Resolution 2.70 Å R-free 0.237
4FWJ Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A Deposited 2012-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.222
4FWJ Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A Deposited 2012-07-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.222
4FWJ Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A Deposited 2012-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–822（793 aa） Fragment：UNP residues 30-822 Chain B 30–822（793 aa） Fragment：UNP residues 30-822	Not recorded	ZN ZINC ION × 6 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 K POTASSIUM ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.222
4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822 Chain C 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.221
4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 51–822（772 aa） Fragment：UNP residues 51-822 Chain D 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.10 Å R-free 0.221
4GU1 Crystal structure of LSD2 Deposited 2012-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.2M Sodium chloride, 0.1M Na/K phosphate, 7% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.94 Å R-free 0.228
4GU1 Crystal structure of LSD2 Deposited 2012-08-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.2M Sodium chloride, 0.1M Na/K phosphate, 7% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.94 Å R-free 0.228
4GU1 Crystal structure of LSD2 Deposited 2012-08-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822 Chain B 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 CL CHLORIDE ION × 4 NA SODIUM ION × 2 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.2M Sodium chloride, 0.1M Na/K phosphate, 7% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.94 Å R-free 0.228
4GUR Crystal structure of LSD2-NPAC with H3 in space group P21 Deposited 2012-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.51 Å R-free 0.204
4GUS Crystal structure of LSD2-NPAC with H3 in space group P3221 Deposited 2012-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 IOD IODIDE ION × 6 GOL GLYCEROL × 2 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1M Ammonium Iodide, 0.1M MES, 10% PEG3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.23 Å R-free 0.237
4GUT Crystal structure of LSD2-NPAC Deposited 2012-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 ZN ZINC ION × 3 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.207
4GUU Crystal structure of LSD2-NPAC with tranylcypromine Deposited 2012-08-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FA9 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(3R,3aS,7aR)-10,11-dimethyl-1,4,6-trioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.231
4HSU Crystal structure of LSD2-NPAC with H3(1-26)in space group P21 Deposited 2012-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 51–822（772 aa） Fragment：UNP residues 51-822	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.99 Å R-free 0.232
6R1U Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2 Deposited 2019-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain K 51–822（772 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.36 Å
6R25 Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3 Deposited 2019-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain K 51–822（772 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.61 Å
7XE1 Crystal structure of LSD2 in complex with cis-4-Br-PCPA Deposited 2022-03-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 DIJ 3-(4-bromophenyl)propanal × 1 FLC CITRATE ANION × 1 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；320mM Ammonium citrate, 22% PEG 3350	Resolution 2.07 Å R-free 0.192
7XE1 Crystal structure of LSD2 in complex with cis-4-Br-PCPA Deposited 2022-03-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 DIJ 3-(4-bromophenyl)propanal × 1 GOL GLYCEROL × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；320mM Ammonium citrate, 22% PEG 3350	Resolution 2.07 Å R-free 0.192
7XE2 Crystal structure of LSD2 in complex with trans-4-Br-PCPA Deposited 2022-03-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DIJ 3-(4-bromophenyl)propanal × 2 FLC CITRATE ANION × 1 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；300mM Ammonium citrate, 24% PEG 3350	Resolution 2.05 Å R-free 0.194
7XE2 Crystal structure of LSD2 in complex with trans-4-Br-PCPA Deposited 2022-03-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 30–822（793 aa）	Not recorded	ZN ZINC ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DIJ 3-(4-bromophenyl)propanal × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；288 K；300mM Ammonium citrate, 24% PEG 3350	Resolution 2.05 Å R-free 0.194

14 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KDM1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–793； UniProt 30–822 Author chain B； PDBConstruct 1–793； UniProt 30–822

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7xe3
Deposition date deposition_date	2022-03-29
Structure title title	Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024)
Keywords keywords	DEMETHYLASE, AMINE OXIDASE, CHROMATIN, HISTONE, FAD, MECHANISM-BASED INHIBITOR, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	38.90 Å
Radius of gyration Rg (electron density) rg_electron	38.32 Å
Forward intensity I(0) i0	437279000.00
Molecular weight molecular_weight	170160.0 kDa
Excluded volume excluded_volume	212610 Å³
Envelope volume envelope_volume	278140 Å³
Hydration-shell volume shell_volume	60320 Å³
Envelope diameter envelope_diameter	137.9 Å
Shell Rg shell_rg	44.50 Å
Envelope Rg envelope_rg	37.77 Å
Shape Rg shape_rg	38.32 Å
Total Rg total_rg	38.67 Å
Total atoms total_atoms	11930
Residues n_residues	1489
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	128.5 Å
Rg (real space) rg_real	38.77 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	4.3730e+08
I(0) uncertainty (real space) i0_real_error	6.7300e+06
Rg (reciprocal space) rg_reciprocal	38.85 Å
I(0) (reciprocal space) i0_reciprocal	437300000.0000
Solution quality estimate total_estimate	0.8861
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	50.1 Å
Skewness Skewness skewness	0.227
Kurtosis Kurtosis kurtosis	-0.357
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	71230000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.887

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Lysine-specific histone demethylase 1B
Molecular weight formula_weight	89014.6 kDa
EC 编号 ec_number	1.14.99.66
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	12142

AKKKATETTDEDEDGGSEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal
Molecular weight formula_weight	249.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	212

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8. Citations (1)

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Unit-cell length a length_a	143.372 Å
Unit-cell length b length_b	171.226 Å
Unit-cell length c length_c	201.918 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	orthorhombic

Resolution resolution	2.820 Å
Low-resolution limit resolution_low	48.270 Å
R factor r_factor	0.1790
R_work r_work	0.1770
R_free r_free	0.2220

fit	/app/data/saxs_computation/xe/7xe3/7xe3.fit
pddf	/app/data/pr_computation/xe/7xe3/7xe3.pr.out
profile	/app/data/saxs_computation/xe/7xe3/7xe3.dat

Crystal structure of LSD2 in complex with cis-4-Br-2,5-F2-PCPA (S1024)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Lysine-specific histone demethylase 1B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction